Align lysine-specific permease (characterized)
to candidate Pf6N2E2_5633 Aromatic amino acid transport protein AroP
Query= CharProtDB::CH_091040 (611 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Length = 472 Score = 243 bits (619), Expect = 2e-68 Identities = 150/461 (32%), Positives = 236/461 (51%), Gaps = 22/461 (4%) Query: 106 VKRALKQRHIGMIALGGTIGTGLFVGISTPLSNAGPVGSLIAYIFMGTIVYFVTQSLGEM 165 +KR LK RHI +IALGG IGTGLF+G + L +AGP ++ Y G I + + + LGEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAICGFIAFMIMRQLGEM 69 Query: 166 ATFIPVTSSITVFSKRFLSPAFGVSNGYMYWFNWAITYAVEVSVIGQVIEYWTDKVPLAA 225 PV S + F+ ++ G +G+ W + + E++ +G+ I YW +P Sbjct: 70 IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129 Query: 226 WIAIFWVIITLMNFFPVKVYGEFEFWVASVKVLAIMGYLIYALIIVCGGSHQGPIG--FR 283 A F+++I ++N VKV+GE EFW A +KV+AI+G + ++ G H GP Sbjct: 130 SAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSG-HGGPQASVTN 188 Query: 284 YWRNPGAWGPGIISSDKSEGRFLGWVSSLINAAFTYQGTELVGITAGEAANPRKTVPRAI 343 W + G + G+ G V ++ F++ G E++G TA EA P+ +P+AI Sbjct: 189 LWSHGGFFPNGV----------SGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAI 238 Query: 344 NKVVFRIVLFYIMSLFFIGLLVPYND--SRLSASSAVIASSPFVISIQNAGTYALPDIFN 401 N+V++RI++FYI +L + L P++ S L+AS + SPFV G+ I N Sbjct: 239 NQVIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILN 298 Query: 402 AVVLITVVSAANSNVYVGSRVLYSLARTGNAPKQFGYVTRQGVPYLGVVCTAALGLLAFL 461 VVL +S NS Y SR+L +A G+APK + ++GVP ++ +AA+ L+A L Sbjct: 299 FVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVAVL 358 Query: 462 VVNNNANTAFNWLINISTLAGLCAWLFISLAHIRFMQALKHRGISRDDLPFKAKLMPYGA 521 + A L+++ + W IS +H +F Q H + FKA PYG Sbjct: 359 LNYLIPQHALELLMSLVVATLVINWAMISYSHFKFRQ---HMNQTHQTPLFKALWYPYGN 415 Query: 522 YYAAFFVTVIIFIQGFQAFCPFKVSEFFTSYISLILLAVVF 562 Y FV +FI G P + + ++ +AV + Sbjct: 416 YICLAFV---VFILGVMLLIPGIQVSVYAIPVWVVFMAVCY 453 Lambda K H 0.324 0.138 0.426 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 727 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 611 Length of database: 472 Length adjustment: 35 Effective length of query: 576 Effective length of database: 437 Effective search space: 251712 Effective search space used: 251712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory